Variant report

Variant	rs7793921
Chromosome Location	chr7:56120881-56120882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56117687-56123706	K562	blood:	n/a	n/a
2	POLR2A	chr7:56120847-56122610	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:56120765-56123238	K562	blood:	n/a	n/a
4	POLR2A	chr7:56120570-56122744	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr7:56117608-56122645	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:56120880-56122484	HepG2	liver:	n/a	n/a
7	MAFK	chr7:56120849-56121806	K562	blood:	n/a	chr7:56121273-56121288
8	POLR2A	chr7:56120539-56122029	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr7:56117175-56121009	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:56120491-56122456	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr7:56117859-56122614	K562	blood:	n/a	n/a
12	IRF1	chr7:56120815-56121283	K562	blood:	n/a	n/a
13	POLR2A	chr7:56120622-56122531	K562	blood:	n/a	n/a
14	POLR2A	chr7:56117844-56122283	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr7:56117697-56122605	GM12891	blood:	n/a	n/a
16	POLR2A	chr7:56117565-56122648	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr7:56117650-56122140	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr7:56120867-56121475	HepG2	liver:	n/a	n/a
19	POLR2A	chr7:56120730-56120891	ProgFib	skin:	n/a	n/a
20	POLR2A	chr7:56120572-56120884	K562	blood:	n/a	n/a
21	BHLHE40	chr7:56120874-56121461	K562	blood:	n/a	n/a
22	POLR2A	chr7:56117529-56122526	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56119419..56122353-chr8:107669214..107670843,2	MCF-7	breast:
2	chr7:56029925..56033959-chr7:56116899..56121286,8	MCF-7	breast:
3	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
4	chr7:56100273..56103332-chr7:56118092..56121325,5	MCF-7	breast:

No data

Variant related genes	Relation type
PSPH	TF binding region
CCT6A	TF binding region
ENSG00000206603	TF binding region
ENSG00000164830	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000253582	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10081373	0.80[ASN][1000 genomes]
rs10229446	0.84[ASW][hapmap]
rs10255049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238394	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11771788	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11773374	0.87[ASN][1000 genomes]
rs11773453	0.87[ASN][1000 genomes]
rs12669623	0.85[AMR][1000 genomes]
rs13234899	0.89[ASN][1000 genomes]
rs13241866	0.80[GIH][hapmap]
rs13244654	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2016724	0.84[CHB][hapmap]
rs2230197	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2242508	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2908543	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2908544	0.86[ASN][1000 genomes]
rs2908545	0.86[ASN][1000 genomes]
rs2908550	0.86[ASN][1000 genomes]
rs3735665	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4049337	0.84[AMR][1000 genomes]
rs4275190	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs4470984	0.84[ASW][hapmap]
rs4543497	0.84[ASW][hapmap]
rs4689	0.84[ASW][hapmap]
rs4947533	0.84[ASW][hapmap]
rs4948096	0.84[ASW][hapmap]
rs4948104	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4948106	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6593297	0.84[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6945795	0.92[ASN][1000 genomes]
rs6954546	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6958480	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6966609	0.84[AMR][1000 genomes]
rs7783339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7801169	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7801467	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7811270	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816408	0.86[ASN][1000 genomes]
rs816409	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs816411	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	esv3425362	chr7:56118483-56121331	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7793921	GBAS	cis	cerebellum	SCAN
rs7793921	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs7793921	GBAS	cis	parietal	SCAN
rs7793921	SUMF2	cis	parietal	SCAN
rs7793921	ZNF713	cis	cerebellum	SCAN
rs7793921	FKBP9L	cis	cerebellum	SCAN
rs7793921	SUMF2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56118000-56121000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:56118800-56121200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:56119800-56121400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr7:56120000-56121200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr7:56120000-56122400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
6	chr7:56120200-56121000	Enhancers	Primary B cells from peripheral blood	blood
7	chr7:56120200-56121000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:56120200-56121400	Transcr. at gene 5' and 3'	NHEK	skin
9	chr7:56120200-56121600	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr7:56120200-56122000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:56120200-56124000	Weak transcription	Spleen	Spleen
12	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
14	chr7:56120400-56121000	Enhancers	Primary B cells from cord blood	blood
15	chr7:56120400-56121000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:56120400-56121000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:56120400-56121000	Enhancers	Liver	Liver
18	chr7:56120400-56121000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr7:56120400-56121000	Enhancers	Fetal Brain Male	brain
20	chr7:56120400-56121000	Genic enhancers	Fetal Lung	lung
21	chr7:56120400-56121000	Enhancers	Stomach Mucosa	stomach
22	chr7:56120400-56121000	Enhancers	Stomach Smooth Muscle	stomach
23	chr7:56120400-56121200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:56120400-56121200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr7:56120400-56121200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:56120400-56121200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:56120400-56121200	Genic enhancers	Brain Cingulate Gyrus	brain
28	chr7:56120400-56121200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:56120400-56121200	Enhancers	Brain Substantia Nigra	brain
30	chr7:56120400-56121200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
31	chr7:56120400-56121200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr7:56120400-56121200	Genic enhancers	Osteobl	bone
33	chr7:56120400-56121400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:56120400-56121400	Enhancers	Pancreas	Pancrea
35	chr7:56120400-56121400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:56120400-56121600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
37	chr7:56120400-56121800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:56120400-56122400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:56120400-56123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:56120400-56123000	Weak transcription	Ovary	ovary
41	chr7:56120400-56124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:56120400-56124000	Weak transcription	Gastric	stomach
43	chr7:56120600-56121000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:56120600-56121000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr7:56120600-56121000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:56120600-56121000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:56120600-56121000	Flanking Active TSS	GM12878-XiMat	blood
48	chr7:56120600-56121000	Flanking Active TSS	K562	blood
49	chr7:56120600-56121200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:56120600-56121200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links